Method of predicting breast cancer prognosis

Abstract

The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient. The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.

1 . A method of predicting a likelihood of long-term survival without recurrence of breast cancer in a breast cancer patient, comprising:
 determining a level of one or more breast cancer prognostic biomarkers in a breast cancer tumor sample obtained from the patient, wherein the one or more breast cancer prognostic biomarkers is selected from:   (a) one or more RNA transcripts, or expression products thereof, selected from Table 1 and/or Table 15,   (b) one or more RNA transcripts, or expression products thereof, selected from Table 2,   (c) one or more intronic RNAs selected from Table 3,   (d) one or more long intergenic non-coding regions (lincRNAs) selected from Table 4,   (e) one or more intergenic sequences selected from Table 5,   (f) one or more intergenic regions selected from intergenic regions 1-69 in Table 5,   (g) one or more RNA transcripts, or expression products thereof, selected from Tables 6-11, and   (h) one or more RNA transcripts, or expression products thereof, selected from Table 13, normalizing the level of the one or more breast cancer prognostic biomarkers to obtain a normalized level of the one or more breast cancer prognostic biomarkers; and   predicting a likelihood of long-term survival without recurrence of breast cancer of said patient, wherein an increased normalized level of the one or more breast cancer prognostic biomarkers is negatively correlated with an increased likelihood of long-term survival without recurrence of breast cancer if the direction of association of the breast cancer prognostic biomarker is marked 1 in Tables 1, 2, 3, 4, 5, or 15, and wherein an increased normalized level of the one or more breast cancer prognostic biomarker is positively correlated with an increased likelihood of long-term survival without recurrence of breast cancer if the direction of association of the one or more breast cancer prognostic biomarker is marked −1 in Tables 1, 2, 3, 4, 5, or 15.   
     
     
         2 .- 5 . (canceled) 
     
     
         6 . A method of predicting a likelihood of long-term survival without recurrence of breast cancer in a breast cancer patient, comprising:
 determining levels of at least three RNA transcripts, or expression products thereof, in a breast cancer tumor sample obtained from said patient, wherein the at least three RNA transcripts, or expression products thereof, are selected from ENO1, IDH2, TMSB10, PGK1, and G6PD,   normalizing the levels of the at least three RNA transcripts, or expression products thereof, to obtain normalized expression levels of the at least three RNA transcripts or expression products thereof, and   predicting a likelihood of long-term survival without recurrence of breast cancer of said patient using the normalized expression levels, wherein increased normalized expression levels are negatively correlated with an increased likelihood of long-term survival without recurrence of breast cancer.   
     
     
         7 .- 8 . (canceled) 
     
     
         9 . A method of predicting a likelihood of long-term survival without recurrence of breast cancer in a breast cancer patient, comprising:
 determining levels of at least five RNA transcripts, or expression product thereof, in a breast cancer tumor sample obtained from said patient, wherein the at least five RNA transcripts, or expression products thereof, are selected from PGD, TKT, TALDO1, G6PD, GP1, SLC1A5, SLC7A5, OGDH, SUCLG1, ENO1, PGK1, IDH2, ACO2, and FBP1,   normalizing the levels of the at least five RNA transcripts, or expression products thereof, to obtain normalized expression levels of the at least five RNA transcripts or expression products thereof, and   predicting a likelihood of long-term survival without recurrence of breast cancer of said patient using the normalized expression levels, wherein increased normalized expression levels of PGD, TKT, TALDO1, G6PD, GP1, SLC1A5, SLC7A5, OGDH, SUCLG1, ENO1, PGK1, IDH2, and ACO2 are negatively correlated with an increased likelihood of long-term survival without recurrence of breast cancer, and increased normalized expression level of FBP1 is positively correlated with an increased likelihood of long-term survival without recurrence of breast cancer.   
     
     
         10 .- 16 . (canceled)